cnetplotJam: Create a cnetplot igraph object

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Create a cnetplot igraph object

Description

Create a cnetplot igraph object

Usage

cnetplotJam(
  x,
  showCategory = 5,
  categorySize = "geneNum",
  nodeLabel = c("Name", "Description", "ID"),
  foldChange = NULL,
  fixed = TRUE,
  doPlot = FALSE,
  categoryColor = "#E5C494",
  geneColor = "#B3B3B3",
  normalizeGeneSize = TRUE,
  labelCex = 0.45,
  colorSub = NULL,
  verbose = FALSE,
  ...
)

Arguments

x	enrichResults object
showCategory	integer number of categories to include in the resulting Cnet plot.
categorySize	character value indicating how to size the pathway nodes, where "geneNum" sizes nodes by the number of genes in that pathway, and "pvalue" sizes nodes by the enrichment P-value using the format -log10(pvalue).
nodeLabel	character value indicating which colname in as.data.frame(x) to use as a node label. Depending upon the source of data, there may be alternative colnames that are more suitable as node labels.
foldChange	numeric vector named by gene, or NULL. When supplied, the vector names must use the same nomenclature as the x input object, which can be inspected with print(head(x@gene)).
fixed	optional argument passed to netplot.
doPlot	logical indicating whether to plot the result.
categoryColor, geneColor	character color, used to colorize category (pathway) nodes, or gene nodes, respectively.
normalizeGeneSize	logical indicating whether to re-scale the gene node sizes so the mean gene node size is no larger than the median category node size. This option is intended to help gene and category node sizes to be in relative proportion.
labelCex	numeric value to re-scale label text in the igraph object, and is applied directly to the igraph object.
colorSub	character vector of valid R colors, whose names are compared to node names, for example V(g)$name %in% names(colorSub).
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

The purpose of this function is to mimic the steps in DOSE:::cnetplot() except not plot the output, and provide some customizations.

This function calls cnetplot_internalJam(), which among other things adds a node attribute to the resulting igraph, "nodeType", where nodeType="Gene" identifies gene nodes, and nodeType="Set" identifies pathway/gene set nodes.

See Also

Other jam igraph functions: cnet2df(), cnet2im(), cnetplot_internalJam(), color_edges_by_nodegroups(), color_edges_by_nodes_deprecated(), color_edges_by_nodes(), color_nodes_by_nodegroups(), communities2nodegroups(), drawEllipse(), edge_bundle_bipartite(), edge_bundle_nodegroups(), enrichMapJam(), fixSetLabels(), flip_edges(), get_bipartite_nodeset(), igraph2pieGraph(), jam_igraph(), jam_plot_igraph(), label_communities(), layout_with_qfrf(), layout_with_qfr(), mem2emap(), memIM2cnet(), mem_multienrichplot(), nodegroups2communities(), rectifyPiegraph(), relayout_with_qfr(), removeIgraphBlanks(), removeIgraphSinglets(), reorderIgraphNodes(), rotate_igraph_layout(), spread_igraph_labels(), subgraph_jam(), subsetCnetIgraph(), subset_igraph_components(), sync_igraph_communities(), with_qfr()

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.